Create an interface which is similar to the material list box
The example given is called UIList. The following code is based on the Modifier UIList of this answer. Once registered, scene objects can be added, removed, printed or selected via UI Elements.



custom_uilist.py

import bpy

from bpy.props import (IntProperty,
                       BoolProperty,
                       StringProperty,
                       CollectionProperty)

from bpy.types import (Operator,
                       Panel,
                       PropertyGroup,
                       UIList)

# -------------------------------------------------------------------
#   Operators
# -------------------------------------------------------------------

class CUSTOM_OT_actions(Operator):
    """Move items up and down, add and remove"""
    bl_idname = "custom.list_action"
    bl_label = "List Actions"
    bl_description = "Move items up and down, add and remove"
    bl_options = {'REGISTER'}

    action = bpy.props.EnumProperty(
        items=(
            ('UP', "Up", ""),
            ('DOWN', "Down", ""),
            ('REMOVE', "Remove", ""),
            ('ADD', "Add", "")))

    def invoke(self, context, event):
        scn = context.scene
        idx = scn.custom_index

        try:
            item = scn.custom[idx]
        except IndexError:
            pass
        else:
            if self.action == 'DOWN' and idx &lt; len(scn.custom) - 1:
                item_next = scn.custom[idx+1].name
                scn.custom.move(idx, idx+1)
                scn.custom_index += 1
                info = 'Item "%s" moved to position %d' % (item.name, scn.custom_index + 1)
                self.report({'INFO'}, info)

            elif self.action == 'UP' and idx &gt;= 1:
                item_prev = scn.custom[idx-1].name
                scn.custom.move(idx, idx-1)
                scn.custom_index -= 1
                info = 'Item "%s" moved to position %d' % (item.name, scn.custom_index + 1)
                self.report({'INFO'}, info)

            elif self.action == 'REMOVE':
                info = 'Item "%s" removed from list' % (scn.custom[idx].name)
                scn.custom_index -= 1
                scn.custom.remove(idx)
                self.report({'INFO'}, info)

        if self.action == 'ADD':
            if context.object:
                item = scn.custom.add()
                item.name = context.object.name
                item.obj_type = context.object.type
                item.obj_id = len(scn.custom)
                scn.custom_index = len(scn.custom)-1
                info = '"%s" added to list' % (item.name)
                self.report({'INFO'}, info)
            else:
                self.report({'INFO'}, "Nothing selected in the Viewport")
        return {"FINISHED"}


class CUSTOM_OT_printItems(Operator):
    """Print all items and their properties to the console"""
    bl_idname = "custom.print_items"
    bl_label = "Print Items to Console"
    bl_description = "Print all items and their properties to the console"
    bl_options = {'REGISTER', 'UNDO'}

    reverse_order = BoolProperty(
        default=False,
        name="Reverse Order")

    @classmethod
    def poll(cls, context):
        return bool(context.scene.custom)

    def execute(self, context):
        scn = context.scene
        if self.reverse_order:
            for i in range(scn.custom_index, -1, -1):        
                item = scn.custom[i]
                print ("Name:", item.name,"-",item.obj_type,item.obj_id)
        else:
            for item in scn.custom:
                print ("Name:", item.name,"-",item.obj_type,item.obj_id)
        return{'FINISHED'}


class CUSTOM_OT_clearList(Operator):
    """Clear all items of the list"""
    bl_idname = "custom.clear_list"
    bl_label = "Clear List"
    bl_description = "Clear all items of the list"
    bl_options = {'INTERNAL'}

    @classmethod
    def poll(cls, context):
        return bool(context.scene.custom)

    def invoke(self, context, event):
        return context.window_manager.invoke_confirm(self, event)

    def execute(self, context):
        if bool(context.scene.custom):
            context.scene.custom.clear()
            self.report({'INFO'}, "All items removed")
        else:
            self.report({'INFO'}, "Nothing to remove")
        return{'FINISHED'}


class CUSTOM_OT_removeDuplicates(Operator):
    """Remove all duplicates"""
    bl_idname = "custom.remove_duplicates"
    bl_label = "Remove Duplicates"
    bl_description = "Remove all duplicates"
    bl_options = {'INTERNAL'}

    def find_duplicates(self, context):
        """find all duplicates by name"""
        name_lookup = {}
        for c, i in enumerate(context.scene.custom):
            name_lookup.setdefault(i.name, []).append(c)
        duplicates = set()
        for name, indices in name_lookup.items():
            for i in indices[1:]:
                duplicates.add(i)
        return sorted(list(duplicates))

    @classmethod
    def poll(cls, context):
        return bool(context.scene.custom)

    def execute(self, context):
        scn = context.scene
        removed_items = []
        # Reverse the list before removing the items
        for i in self.find_duplicates(context)[::-1]:
            scn.custom.remove(i)
            removed_items.append(i)
        if removed_items:
            scn.custom_index = len(scn.custom)-1
            info = ', '.join(map(str, removed_items))
            self.report({'INFO'}, "Removed indices: %s" % (info))
        else:
            self.report({'INFO'}, "No duplicates")
        return{'FINISHED'}

    def invoke(self, context, event):
        return context.window_manager.invoke_confirm(self, event)


class CUSTOM_OT_selectItems(Operator):
    """Select Items in the Viewport"""
    bl_idname = "custom.select_items"
    bl_label = "Select Item(s) in Viewport"
    bl_description = "Select Items in the Viewport"
    bl_options = {'REGISTER', 'UNDO'}

    select_all = BoolProperty(
        default=False,
        name="Select all Items of List",
        options={'SKIP_SAVE'})

    @classmethod
    def poll(cls, context):
        return bool(context.scene.custom)

    def execute(self, context):
        scn = context.scene
        idx = scn.custom_index

        try:
            item = scn.custom[idx]
        except IndexError:
            self.report({'INFO'}, "Nothing selected in the list")
            return{'CANCELLED'}

        obj_error = False
        bpy.ops.object.select_all(action='DESELECT')
        if not self.select_all:
            obj = scn.objects.get(scn.custom[idx].name, None)
            if not obj: 
                obj_error = True
            else:
                obj.select = True
                info = '"%s" selected in Viewport' % (obj.name)
        else:
            selected_items = []
            unique_objs = set([i.name for i in scn.custom])
            for i in unique_objs:
                obj = scn.objects.get(i, None)
                if obj:
                    obj.select = True
                    selected_items.append(obj.name)

            if not selected_items: 
                obj_error = True
            else:
                missing_items = unique_objs.difference(selected_items)
                if not missing_items:
                    info = '"%s" selected in Viewport' \
                        % (', '.join(map(str, selected_items)))
                else:
                    info = 'Missing items: "%s"' \
                        % (', '.join(map(str, missing_items)))
        if obj_error: 
            info = "Nothing to select, object removed from scene"
        self.report({'INFO'}, info)    
        return{'FINISHED'}


# -------------------------------------------------------------------
#   Drawing
# -------------------------------------------------------------------

class CUSTOM_UL_items(UIList):
    def draw_item(self, context, layout, data, item, icon, active_data, active_propname, index):
        split = layout.split(0.3)
        split.label("Index: %d" % (index))
        custom_icon = "OUTLINER_OB_%s" % item.obj_type
        #split.prop(item, "name", text="", emboss=False, translate=False, icon=custom_icon)
        split.label(item.name, icon=custom_icon) # avoids renaming the item by accident

    def invoke(self, context, event):
        pass   

class CUSTOM_PT_objectList(Panel):
    """Adds a custom panel to the TEXT_EDITOR"""
    bl_idname = 'TEXT_PT_my_panel'
    bl_space_type = "TEXT_EDITOR"
    bl_region_type = "UI"
    bl_label = "Custom Object List Demo"

    def draw(self, context):
        layout = self.layout
        scn = bpy.context.scene

        rows = 2
        row = layout.row()
        row.template_list("CUSTOM_UL_items", "", scn, "custom", scn, "custom_index", rows=rows)

        col = row.column(align=True)
        col.operator("custom.list_action", icon='ZOOMIN', text="").action = 'ADD'
        col.operator("custom.list_action", icon='ZOOMOUT', text="").action = 'REMOVE'
        col.separator()
        col.operator("custom.list_action", icon='TRIA_UP', text="").action = 'UP'
        col.operator("custom.list_action", icon='TRIA_DOWN', text="").action = 'DOWN'

        row = layout.row()
        col = row.column(align=True)
        row = col.row(align=True)
        row.operator("custom.print_items", icon="LINENUMBERS_ON") #LINENUMBERS_OFF, ANIM
        row = col.row(align=True)
        row.operator("custom.select_items", icon="VIEW3D", text="Select Item")
        row.operator("custom.select_items", icon="GROUP", text="Select all Items").select_all = True
        row = col.row(align=True)
        row.operator("custom.clear_list", icon="X")
        row.operator("custom.remove_duplicates", icon="GHOST")


# -------------------------------------------------------------------
#   Collection
# -------------------------------------------------------------------

class CUSTOM_objectCollection(PropertyGroup):
    #name = StringProperty() -&gt; Instantiated by default
    obj_type = StringProperty()
    obj_id = IntProperty()


# -------------------------------------------------------------------
#   Register &amp; Unregister
# -------------------------------------------------------------------

classes = (
    CUSTOM_OT_actions,
    CUSTOM_OT_printItems,
    CUSTOM_OT_clearList,
    CUSTOM_OT_removeDuplicates,
    CUSTOM_OT_selectItems,
    CUSTOM_UL_items,
    CUSTOM_PT_objectList,
    CUSTOM_objectCollection,
)

def register():
    from bpy.utils import register_class
    for cls in classes:
        register_class(cls)

    # Custom scene properties
    bpy.types.Scene.custom = CollectionProperty(type=CUSTOM_objectCollection)
    bpy.types.Scene.custom_index = IntProperty()


def unregister():
    from bpy.utils import unregister_class
    for cls in reversed(classes):
        unregister_class(cls)

    del bpy.types.Scene.custom
    del bpy.types.Scene.custom_index


if __name__ == "__main__":
    register()


Updated for Blender 2.8x: https://gist.github.com/p2or/d6dfd47366b2f14816f57d2067dcb6a9



As of 2.79 we can have real references to objects per ID by using a PointerProperty, which basically allows to display the actual data, access and edit the attributes on the fly.

Following funky example is a simple demo on how to create a custom UIList of materials. You can create new materials, display and edit their properties (name, color etc.) directly within the list.



material_uilist.py

import bpy

from bpy.props import (IntProperty,
                       BoolProperty,
                       StringProperty,
                       CollectionProperty,
                       PointerProperty)

from bpy.types import (Operator,
                       Panel,
                       PropertyGroup,
                       UIList)


def random_color():
    from mathutils import Color
    from random import random
    return Color((random(), random(), random()))

# -------------------------------------------------------------------
#   Operators
# -------------------------------------------------------------------

class CUSTOM_OT_actions(Operator):
    """Move items up and down, add and remove"""
    bl_idname = "custom.list_action"
    bl_label = "List Actions"
    bl_description = "Move items up and down, add and remove"
    bl_options = {'REGISTER'}

    action = bpy.props.EnumProperty(
        items=(
            ('UP', "Up", ""),
            ('DOWN', "Down", ""),
            ('REMOVE', "Remove", ""),
            ('ADD', "Add", "")))

    def invoke(self, context, event):
        scn = context.scene
        idx = scn.custom_index

        try:
            item = scn.custom[idx]
        except IndexError:
            pass
        else:
            if self.action == 'DOWN' and idx &lt; len(scn.custom) - 1:
                item_next = scn.custom[idx+1].name
                scn.custom.move(idx, idx+1)
                scn.custom_index += 1
                info = 'Item "%s" moved to position %d' % (item.name, scn.custom_index + 1)
                self.report({'INFO'}, info)

            elif self.action == 'UP' and idx &gt;= 1:
                item_prev = scn.custom[idx-1].name
                scn.custom.move(idx, idx-1)
                scn.custom_index -= 1
                info = 'Item "%s" moved to position %d' % (item.name, scn.custom_index + 1)
                self.report({'INFO'}, info)

            elif self.action == 'REMOVE':
                item = scn.custom[scn.custom_index]
                item_name = item.material.name
                mat = item.material                
                mat_obj = bpy.data.materials.get(mat.name, None)
                if mat_obj:
                    bpy.data.materials.remove(mat_obj, True)
                info = 'Item %s removed from scene' % (item_name)
                scn.custom.remove(idx)
                scn.custom_index -= 1
                self.report({'INFO'}, info)

        if self.action == 'ADD':
            item = scn.custom.add()
            item.id = len(scn.custom)
            item.material = bpy.data.materials.new(name="Material")
            item.name = item.material.name
            item.material.diffuse_color = random_color()
            scn.custom_index = (len(scn.custom)-1)
            info = '%s added to list' % (item.name)
            self.report({'INFO'}, info)
        return {"FINISHED"}


class CUSTOM_OT_printItems(Operator):
    """Print all items and their properties to the console"""
    bl_idname = "custom.print_items"
    bl_label = "Print Items to Console"
    bl_description = "Print all items and their properties to the console"
    bl_options = {'REGISTER', 'UNDO'}

    reverse_order = BoolProperty(
        default=False,
        name="Reverse Order")

    @classmethod
    def poll(cls, context):
        return bool(context.scene.custom)

    def execute(self, context):
        scn = context.scene
        if self.reverse_order:
            for i in range(scn.custom_index, -1, -1):        
                mat = scn.custom[i].material
                print ("Material:", mat,"-",mat.name, mat.diffuse_color)
        else:
            for item in scn.custom:
                mat = item.material
                print ("Material:", mat,"-",mat.name, mat.diffuse_color)
        return{'FINISHED'}


class CUSTOM_OT_clearList(Operator):
    """Clear all items of the list and remove from scene"""
    bl_idname = "custom.clear_list"
    bl_label = "Clear List and Remove Materials"
    bl_description = "Clear all items of the list and remove from scene"
    bl_options = {'INTERNAL'}

    @classmethod
    def poll(cls, context):
        return bool(context.scene.custom)

    def invoke(self, context, event):
        return context.window_manager.invoke_confirm(self, event)

    def execute(self, context):

        if bool(context.scene.custom):
            # Remove materials from scene
            for i in context.scene.custom:
                name = i.material.name
                mat_obj = bpy.data.materials.get(name, None)
                if mat_obj:
                    bpy.data.materials.remove(mat_obj, True)
                info = 'Item %s removed from scene' % (name)

            # Clear the list
            context.scene.custom.clear()
            self.report({'INFO'}, "All materials removed from scene")
        else:
            self.report({'INFO'}, "Nothing to remove")
        return{'FINISHED'}


# -------------------------------------------------------------------
#   Drawing
# -------------------------------------------------------------------

class CUSTOM_UL_items(UIList):
    def draw_item(self, context, layout, data, item, icon, active_data, active_propname, index):
        mat = item.material
        if self.layout_type in {'DEFAULT', 'COMPACT'}:
            split = layout.split(0.3)
            split.label("Index: %d" % (index))
            # static method UILayout.icon returns the integer value of the icon ID
            # "computed" for the given RNA object.
            split.prop(mat, "name", text="", emboss=False, icon_value=layout.icon(mat))

        elif self.layout_type in {'GRID'}:
            layout.alignment = 'CENTER'
            layout.label(text="", icon_value=layout.icon(mat))

    def invoke(self, context, event):
        pass

class CUSTOM_PT_objectList(Panel):
    """Adds a custom panel to the TEXT_EDITOR"""
    bl_idname = 'TEXT_PT_my_panel'
    bl_space_type = "TEXT_EDITOR"
    bl_region_type = "UI"
    bl_label = "Custom Material List Demo"

    def draw(self, context):
        layout = self.layout
        scn = bpy.context.scene

        rows = 2
        row = layout.row()
        row.template_list("CUSTOM_UL_items", "custom_def_list", scn, "custom", 
            scn, "custom_index", rows=rows)

        col = row.column(align=True)
        col.operator("custom.list_action", icon='ZOOMIN', text="").action = 'ADD'
        col.operator("custom.list_action", icon='ZOOMOUT', text="").action = 'REMOVE'
        col.separator()
        col.operator("custom.list_action", icon='TRIA_UP', text="").action = 'UP'
        col.operator("custom.list_action", icon='TRIA_DOWN', text="").action = 'DOWN'

        row = layout.row()
        row.template_list("CUSTOM_UL_items", "custom_grid_list", scn, "custom", 
            scn, "custom_index", rows=2, type='GRID')

        row = layout.row()
        col = row.column(align=True)
        row = col.row(align=True)
        row.operator("custom.print_items", icon="LINENUMBERS_ON")
        row = col.row(align=True)
        row.operator("custom.clear_list", icon="X")


# -------------------------------------------------------------------
#   Collection
# -------------------------------------------------------------------

class CUSTOM_objectCollection(PropertyGroup):
    #name = StringProperty() -&gt; Instantiated by default
    material = PointerProperty(
        name="Material",
        type=bpy.types.Material)

# -------------------------------------------------------------------
#   Register &amp; Unregister
# -------------------------------------------------------------------

classes = (
    CUSTOM_OT_actions,
    CUSTOM_OT_printItems,
    CUSTOM_OT_clearList,
    CUSTOM_UL_items,
    CUSTOM_PT_objectList,
    CUSTOM_objectCollection,
)

def register():
    from bpy.utils import register_class
    for cls in classes:
        register_class(cls)

    # Custom scene properties
    bpy.types.Scene.custom = CollectionProperty(type=CUSTOM_objectCollection)
    bpy.types.Scene.custom_index = IntProperty()


def unregister():
    from bpy.utils import unregister_class
    for cls in reversed(classes):
        unregister_class(cls)

    del bpy.types.Scene.custom
    del bpy.types.Scene.custom_index


if __name__ == "__main__":
    register()


Updated for Blender 2.8x: https://gist.github.com/p2or/30b8b30c89871b8ae5c97803107fd494

Same principle applies to all other types. Using the PointerProperty for e.g. objects in the scene, makes it pretty comfortable to edit, add and remove them safely without any additional checks.